A5091482362- Forensic and Genetic Research
- Genetic diversity and population structure
- Race, Genetics, and Society
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Archaeology and ancient environmental studies
- Genetic Associations and Epidemiology
- Genetic Mapping and Diversity in Plants and Animals
- Evolution and Paleontology Studies
- Fish Biology and Ecology Studies
- Hepatitis B Virus Studies
- BRCA gene mutations in cancer
- Diabetes and associated disorders
- Fish Ecology and Management Studies
- Pacific and Southeast Asian Studies
- Molecular Biology Techniques and Applications
- Rangeland Management and Livestock Ecology
- Aquatic Ecosystems and Biodiversity
- Evolution and Genetic Dynamics
- Forensic Anthropology and Bioarchaeology Studies
Rutgers, The State University of New Jersey
2005-2018
Biolog (United States)
2014
University of California, Berkeley
2009-2014
Integra (United States)
2009-2014
Evolutionary Genomics (United States)
2014
Consejo Nacional de Investigaciones Científicas y Técnicas
2014
Stanford University
2014
Pennsylvania State University
2014
Natural History Museum Aarhus
2014
University of Copenhagen
2014
We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, represents a male individual first known culture to settle in Greenland. Sequenced average depth 20×, we recover 79% diploid genome, amount close practical limit current sequencing technologies. identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), which 6.8% have not been reported previously. estimate raw read contamination be no higher than 0.8%. use...
Whole-genome data indicate that early modern humans expanded into Australia 62,000 to 75,000 years ago.
The New World Arctic, the last region of Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans Greenland, Arctic Canada, Alaska, Aleutian Islands, Siberia. show that Paleo-Eskimos (~3000 BCE 1300 CE) represent migration pulse into independent both Native American Inuit expansions. Furthermore, continuity characterizing Paleo-Eskimo period...
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with state space that includes all possible phylogenies in full Isolation-with-Migration model framework. The based on new type of genealogy augmentation called "hidden genealogy" enables efficient updating the phylogeny. This first likelihood-based to fully incorporate directional gene flow genetic...
Despite strides in characterizing human history from genetic polymorphism data, progress identifying signatures of recent demography has been limited. Here we identify very fine-scale population structure North America a network over 500 million (identity-by-descent, IBD) connections among 770,000 genotyped individuals US origin. We detect densely connected clusters within the and annotate these using database 20 genealogical records. Recent patterns captured by IBD clustering include...
The cichlid fishes of Lake Malawi are famously diverse. However, phylogenetic and population genetic studies their history have been difficult because the great amount variation that is shared between species. We apply a recently developed method for fitting “isolation with migration” divergence model to data set specially designed compound loci develop portraits species divergence. Outgroup sequences from Tanganyika permit parameter estimates in units years effective sizes. Estimated...
Most methods for studying divergence with gene flow rely upon data from many individuals at few loci. Such can be useful inferring recent population history but they are unlikely to contain sufficient information about older events. However, the growing availability of genome sequences suggests a different kind sampling scheme, one that may more suited relatively ancient divergence. Data sets extracted whole-genome alignments represent very large number To take advantage such we developed...
Abstract Summary: We present bammds , a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with reference panel individuals (usually genotypes) using multidimensional scaling algorithm. Our is aimed at determining the ancestry unknown samples—typical ancient DNA data—particularly only low amounts data are available for those samples. Availability and implementation: The software package under GNU General Public License v3 freely...
The cichlid fishes of Lake Malawi are famously diverse. However, evolutionary studies have been difficult because their recent and uncertain phylogenetic history. Portions 12 nuclear loci were sequenced in nine rock-dwelling species (mbuna) three representatives pelagic nonmbuna species. In contrast to the pattern variation at mitochondrial genes, which do provide resolution level mbuna versus nonmbuna, among some genera, virtually devoid signal. Only a small minority variable positions...
Abstract The inference of population divergence times and branching patterns is fundamental importance in many genetic analyses. Many methods have been developed for estimating times, recently, there has particular attention towards genome‐wide single‐nucleotide polymorphisms (SNP) data. However, most SNP data affected by an ascertainment bias caused the selection discovery protocols. Here, we present a modification existing maximum likelihood method that will allow approximately unbiased...
Abstract Background We present ARCHes, a fast and accurate haplotype-based approach for inferring an individual’s ancestry composition. Our works by modeling haplotype diversity from large, admixed cohort of hundreds thousands, then annotating those models with population information reference panels known ancestry. Results The running time ARCHes does not depend on the size panel because training testing are separate processes, inferred population-annotated can be written to disk reused...
Abstract There is long-standing tension regarding whether and how to use race or geographic ancestry in biomedical research. We examined multiple self-reported measures of from a cohort over 100,000 U.S. residents alongside genetic data. found that these are often non-overlapping, no single measure alone provides better fit than combination including both ancestry. also patterns reporting for appear be influenced by participation direct-to-consumer testing. Our results demonstrate there...
Abstract We present ARCHes, a fast and accurate haplotype-based approach for inferring an individual’s ancestry composition. Our works by modeling haplotype diversity from large, admixed cohort of hundreds thousands, then annotating those models with population information reference panels known ancestry. The running time ARCHes does not depend on the size panel because training testing are separate processes, inferred population-annotated can be written to disk reused label large test sets...